Marvel fought CAPCOM, DC fought Mortal Kombat/Warner Games/Midway (next Injustice game can throw in Rampage monsters, Sinistar, a Knight on an Ostrich, etc., sure), the Ninja Turtles fought uhh Rabbids and Nickelodeon. Sure. What other "comic company VS a video gamer company/series" thing could there be?
Image Comics, I'd place up against either Namco-Bandai, due to preexisting crossovers (Negan in Tekken 7, Spawn in Soul Calibur 2), or ArcSys, given Guilty Gear feels like edgy 90's anime stuff of a sort and that'd match well with Spawn and Battle Chasers, at least. I'd kind of like to see those characters, Savage Dragon, Witchblade, the Darkness, Invincible, Shadowhawk, etc. filtered through that flashy anime style. I guess a version of that for Witchblade sort of exists already. Huh.
Dark Horse Comics feels like it has a dark edge to it with things like Hellboy, the Mask (in the original comics), Ghost, Grendel, Concrete, etc., but has a different sort of vibe to it than what you'd think of for Image's 90's output. It's apparently owned by a video game company now? They own...Gearbox and THQ, I guess. I have not much clue here. The only things I sort of know from Gearbox are Borderlands and Duke Nukem, I think? Duke probably fits pretty well in the Image roster, unless you remember Barb Wire. I guess if I were to go with one, I'd pick Namco if Image takes ArcSys. Usagi Yojimbo kind of fits alongside the likes of Yoshimitsu and Taki, I suppose. Then again, both Image and Dark Horse have a bunch of characters that kind of switch around from publisher to publisher, mostly because they both have a "creator owns the character" policy, for the most part. That's an over-simplification, and they sometimes have their own issues, to say the least, but it's at least a bit better than Marvel and DC's policies. Anyways...
Perhaps the true way to represent this and do an indie spiritual successor to Marvel VS CAPCOM is to take whoever ends up in Fraymakers/games like Fraymakers and pit them up against whoever you can get from this:
https://comicvine.gamespot.com/war-of-the-independents/4050-45034/ MVC-type game with the Tick, Gumby, and SCUD the Disposable Assassin VS Shovel Knight, Commander Video, and OctoDad? Sure, why not?
IDW is mostly licenses, BOOM Studios is mostly licenses, I am doubting either will do big crossover games with all of those licenses, as tempting as Optimus Prime VS Sonic VS Judge Dredd or RoboCop VS Power Rangers VS John McClane sounds. Not really much coherent here. Hasbro VS someone, sure. Judge Dredd/RoboCop crossover? Makes sense. SEGA VS Archie, since they have a past together? Most of Archie's roster by itself is humans (who sometimes get involved with weird things, don't get me wrong), a witch, and a bunch of superheroes you've never heard of. So it's either mostly non-combatants or mostly obscurities. Your mileage may vary.
Scott Pilgrim had a successful enough video game, some even like it a bit more than the comic or movie (I think all three are pretty alright). Maybe they can cross over with River City Girls/Ransom, which is owned by...ArcSys. Go figure.
Type-Moon VS King Features Syndicate. Apparently licensing for Popeye costs very little. I'm just throwing random things against the wall now. But a comic strip characters fighting game would be fun. Garfield's probably not gonna be in it, though, because he's busy. He crossed over with Cuphead, as well, sort of. Maybe King Features VS Microsoft instead? The fight we've all been waiting to see: the Phantom VS Voodoo Vince. Certainly.
I don't exactly know where I'm going with all this. A new TMNT fighter would be neat. Maybe just do that, and later on the Street Sharks, Battletoads, etc. can be guest DLC.
None of this is likely, I realize. Don't worry about it.